Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate 5210398 Shew_2839 carbamoyl phosphate synthase small subunit (RefSeq)
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__PV4:5210398 Length = 390 Score = 602 bits (1552), Expect = e-177 Identities = 297/382 (77%), Positives = 323/382 (84%), Gaps = 1/382 (0%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 + KSALLVLEDGT F G AIGA G AVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI Sbjct: 10 LTKSALLVLEDGTVFSGTAIGADGLAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 69 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GN GTN D ES VHA GL+IRDLPL+ASNFRN + LS YLK +N+V IADIDTRKLTR Sbjct: 70 GNTGTNSEDTESEAVHACGLIIRDLPLLASNFRNEQSLSDYLKSNNVVGIADIDTRKLTR 129 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQ G I+ GD D A AL A+AFPGL GMDLAKEVTT + Y W GSW L GG Sbjct: 130 ILREKGAQAGAILVGDM-DEAKALAAAKAFPGLKGMDLAKEVTTQKQYQWRSGSWRLVGG 188 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 LP E EL + VVAYD+G KRNILRMLVDRGC +T+VPAQT A +VL MNPDGIFLSN Sbjct: 189 LPSDTPESELKYKVVAYDYGVKRNILRMLVDRGCDVTVVPAQTPAAEVLAMNPDGIFLSN 248 Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 GPGDP PCDYAI AIQ FL+TDIP+FGICLGHQLLALASGAKT+KMKFGHHG NHPV ++ Sbjct: 249 GPGDPEPCDYAIEAIQAFLKTDIPLFGICLGHQLLALASGAKTLKMKFGHHGANHPVSNL 308 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 EK VMIT+QNHGFA DE +LPAN++VTHKSLFDG+LQGIH TDKPAFSFQGHPEASPGP Sbjct: 309 EKGNVMITSQNHGFAADETSLPANVKVTHKSLFDGSLQGIHLTDKPAFSFQGHPEASPGP 368 Query: 361 HDAAPLFDHFIELIEQYRKTAK 382 HDAAPLFDHFIELIE+YR AK Sbjct: 369 HDAAPLFDHFIELIEEYRHNAK 390 Lambda K H 0.318 0.135 0.400 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 539 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 382 Length of database: 390 Length adjustment: 30 Effective length of query: 352 Effective length of database: 360 Effective search space: 126720 Effective search space used: 126720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate 5210398 Shew_2839 (carbamoyl phosphate synthase small subunit (RefSeq))
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01368.hmm # target sequence database: /tmp/gapView.31419.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01368 [M=361] Accession: TIGR01368 Description: CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-154 500.5 0.0 1.4e-154 500.3 0.0 1.0 1 lcl|FitnessBrowser__PV4:5210398 Shew_2839 carbamoyl phosphate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5210398 Shew_2839 carbamoyl phosphate synthase small subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 500.3 0.0 1.4e-154 1.4e-154 1 360 [. 14 383 .. 14 384 .. 0.97 Alignments for each domain: == domain 1 score: 500.3 bits; conditional E-value: 1.4e-154 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglvv 78 a lvledGtvf+g+++ga++ +vGevvFnTsmtGYqEiltDpsY++qiv+ltyp+ign+g+n+ed+es+ +++ gl++ lcl|FitnessBrowser__PV4:5210398 14 ALLVLEDGTVFSGTAIGADGLAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNTGTNSEDTESEAVHACGLII 91 579*************************************************************************** PP TIGR01368 79 kelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespkvkevnlvke 156 ++l +sn+r+++sL+++lk++++v+i+++DTR+l++ lRekg+++++i ++++ ++ ++ak+ p +k+++l+ke lcl|FitnessBrowser__PV4:5210398 92 RDLPLLASNFRNEQSLSDYLKSNNVVGIADIDTRKLTRILREKGAQAGAILVGDMDEAKALAAAKAFPGLKGMDLAKE 169 ****************************************************************************** PP TIGR01368 157 vstkeayeleq...........kakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgills 223 v+t+++y++++ ++ +++ k++vv++d+GvK+nilr+Lv+rg++vtvvpa+t+a+e+ ++npdgi+ls lcl|FitnessBrowser__PV4:5210398 170 VTTQKQYQWRSgswrlvgglpsDTPESELKYKVVAYDYGVKRNILRMLVDRGCDVTVVPAQTPAAEVLAMNPDGIFLS 247 **********987777666554356666679*********************************************** PP TIGR01368 224 nGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavd 301 nGPGdP+ +++aie ++++l+++iP+fGIclGhqllala+gakt+k+kfGh+GaNhpv +l++g+v+itsqNHg+a d lcl|FitnessBrowser__PV4:5210398 248 NGPGDPEPCDYAIEAIQAFLKTDIPLFGICLGHQLLALASGAKTLKMKFGHHGANHPVSNLEKGNVMITSQNHGFAAD 325 ****************************************************************************** PP TIGR01368 302 eeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 e sl+++ ++vth++l+Dg+++g++ +++p+fs Q HPeaspGphd++ lFd+f+eli+ lcl|FitnessBrowser__PV4:5210398 326 ETSLPAN-VKVTHKSLFDGSLQGIHLTDKPAFSFQGHPEASPGPHDAAPLFDHFIELIE 383 ***8866.************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (390 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.99 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory